/*
 * CodonFitnessFunction.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.simulator.fitnessfunctions;

import dr.simulator.datatypes.GeneticCode;
import dr.simulator.datatypes.AminoAcids;

public class CodonFitnessFunction extends AbstractFitnessFunction {
	/**
	 * selection coefficients are gamma distributed with parameters alpha and beta
	 */
	public CodonFitnessFunction(int codonCount, GeneticCode geneticCode, FitnessFunction aminoAcidFitnessFunction) {

		int stateSize = 64;

        double[][] logFitnessTable = new double[codonCount][stateSize];

		for (int i = 0; i < codonCount; i++) {

			for (byte j = 0; j < stateSize; j++) {
                byte aminoAcid = (byte)geneticCode.getAminoAcidState(j);

                if (aminoAcid == AminoAcids.STOP_STATE) {
                    // stop codons are lethal
                    logFitnessTable[i][j] = Double.NEGATIVE_INFINITY;
                } else {
				    logFitnessTable[i][j] = aminoAcidFitnessFunction.getLogFitness(i, aminoAcid);
                }
			}
		}

        setLogFitnessTable(logFitnessTable);
  	}

}